Commit 880abf7d authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

should-get-tests/*.should-get: replace $VIDJIL_DIR/data by $VIDJIL_DATA

See #2611.
parent 35525c10
!NO_LAUNCHER:
!LAUNCH: (cd $VIDJIL_DIR/data ; md5sum *.fasta || md5 -r *.fasta)
!LAUNCH: (cd $VIDJIL_DATA ; md5sum *.fasta || md5 -r *.fasta)
$ Check md5 in data/
1:985219d9156b6d9e8966807595beada3 Stanford_S22.fa
......
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -r 1 -k 4 -w 20 -z 0 -c clones -V $VIDJIL_DIR/data/toy_V.fa -J $VIDJIL_DIR/data/toy_J.fa $VIDJIL_DIR/data/ambiguous_representative.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -r 1 -k 4 -w 20 -z 0 -c clones -V $VIDJIL_DATA/toy_V.fa -J $VIDJIL_DATA/toy_J.fa $VIDJIL_DATA/ambiguous_representative.fa
$ Short reads properly segmented
1:SEG_+.* -> .* 4
......
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -c clones -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DIR/data/test_representatives.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -c clones -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/test_representatives.fa
$ Three clones should be found
1:3 clones
......
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c segment -3 -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG $VIDJIL_DIR/data/cdr3-stopcodon.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c segment -3 -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG $VIDJIL_DATA/cdr3-stopcodon.fa
!LOG: out/cdr3-stopcodon.vidjil
$ Two identical junctions in JSON
......
!LAUNCH: export REQUEST_METHOD=POST ; export CONTENT_TYPE=test ; $LAUNCHER $VIDJIL_DIR/browser/cgi/align.cgi < $VIDJIL_DIR/data/msa.fa
!LAUNCH: export REQUEST_METHOD=POST ; export CONTENT_TYPE=test ; $LAUNCHER $VIDJIL_DIR/browser/cgi/align.cgi < $VIDJIL_DATA/msa.fa
$ no spurious info
0: .* bp in .* sequences
......
!LAUNCH: export REQUEST_METHOD=POST ; export CONTENT_TYPE=test ; $LAUNCHER $VIDJIL_DIR/browser/cgi/align.cgi < $VIDJIL_DIR/data/msa2.fa
!LAUNCH: export REQUEST_METHOD=POST ; export CONTENT_TYPE=test ; $LAUNCHER $VIDJIL_DIR/browser/cgi/align.cgi < $VIDJIL_DATA/msa2.fa
$ no spurious info
0: .* bp in .* sequences
......
!LAUNCH: export REQUEST_METHOD=POST ; export CONTENT_TYPE=test ; $LAUNCHER $VIDJIL_DIR/browser/cgi/align.cgi < $VIDJIL_DIR/data/msa3.fa
!LAUNCH: export REQUEST_METHOD=POST ; export CONTENT_TYPE=test ; $LAUNCHER $VIDJIL_DIR/browser/cgi/align.cgi < $VIDJIL_DATA/msa3.fa
$ no spurious info
0: .* bp in .* sequences
......
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -t 0 -g $VIDJIL_DIR/germline -2 $VIDJIL_DIR/data/chimera-fake.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -t 0 -g $VIDJIL_DIR/germline -2 $VIDJIL_DATA/chimera-fake.fa
$ The KmerSegmenter segments the three chimera reads on PSEUDO_MAX12 germline (-2)
1:unexpected .* -> .* 3
......
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline -2 $VIDJIL_DIR/data/chimera-fake-D.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline -2 $VIDJIL_DATA/chimera-fake-D.fa
$ The KmerSegmenter segments the chimera reads on PSEUDO_MAX12 germline (-2)
f1:unexpected .* -> .* 2
......
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/data/chimera-fake-VJ-trim.g $VIDJIL_DIR/data/chimera-fake-VJ.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DATA/chimera-fake-VJ-trim.g $VIDJIL_DATA/chimera-fake-VJ.fa
# Testing a custom (fake) .g with special parameters for the algorithm
$ The KmerSegmenter segments no read in Y because of the parameter
......
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/data/chimera-fake-VJ.g $VIDJIL_DIR/data/chimera-fake-VJ.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DATA/chimera-fake-VJ.g $VIDJIL_DATA/chimera-fake-VJ.fa
# Testing a custom (fake) germlines.data
$ Report the species
......
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline -2 $VIDJIL_DIR/data/chimera-fake-VJ.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline -2 $VIDJIL_DATA/chimera-fake-VJ.fa
$ The KmerSegmenter segments the five chimera reads on PSEUDO_MAX12 germline (-2)
1:unexpected .* -> .* 5
......
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -e 100 -A -t 0 -g $VIDJIL_DIR/germline -4 $VIDJIL_DIR/data/chimera-fake-half.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -e 100 -A -t 0 -g $VIDJIL_DIR/germline -4 $VIDJIL_DATA/chimera-fake-half.fa
# TODO: a more precise modeling should give a e-value computation that could make this work even with -e 1
$ The KmerSegmenter segments the six chimera reads on PSEUDO_MAX1U germline (-4)
......
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline $VIDJIL_DIR/data/chimera-fake.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline $VIDJIL_DATA/chimera-fake.fa
$ Do not segment on any germline, even incomplete
1:junction detected in 0 reads
......
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -uU -g $VIDJIL_DIR/germline $VIDJIL_DIR/data/chimera-trg.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -uU -g $VIDJIL_DIR/germline $VIDJIL_DATA/chimera-trg.fa
$ Do not segment on IGL by chance
f1:IGL .* -> .* 0
......
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG -c clones -A -3 $VIDJIL_DIR/data/segment_lec.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG -c clones -A -3 $VIDJIL_DATA/segment_lec.fa
$ Extract 50bp windows (TRG)
1:found . 50-windows
......
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -k 14 -w 50 -c clones -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -y 3 -z 1 -r 1 $VIDJIL_DIR/data/clones_simul.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -k 14 -w 50 -c clones -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -y 3 -z 1 -r 1 $VIDJIL_DATA/clones_simul.fa
$ Junction extractions
1:found 25 50-windows in 66 reads
......
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -k 14 -w 50 -c clones -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -y 3 -z 0 -r 1 -n 5 $VIDJIL_DIR/data/clones_simul.fa ; cat out/clones_simul.vidjil
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -k 14 -w 50 -c clones -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -y 3 -z 0 -r 1 -n 5 $VIDJIL_DATA/clones_simul.fa ; cat out/clones_simul.vidjil
$ Window extractions
2:found 25 50-windows in 66 reads
......
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -KA -z 0 -s \\\\#\\\\#\\\\#\\\\#\\\\#-\\\\#\\\\#\\\\#\\\\#\\\\# -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -D $VIDJIL_DIR/germline/homo-sapiens/IGHD.fa $VIDJIL_DIR/data/common-V-D.fa ; cat out/common-V-D.affects
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -KA -z 0 -s \\\\#\\\\#\\\\#\\\\#\\\\#-\\\\#\\\\#\\\\#\\\\#\\\\# -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -D $VIDJIL_DIR/germline/homo-sapiens/IGHD.fa $VIDJIL_DATA/common-V-D.fa ; cat out/common-V-D.affects
$ Segments the sequence
1: SEG .* -> .* 1
......
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -3 -c segment -g $VIDJIL_DIR/germline/mus-musculus.g $VIDJIL_DIR/data/example_mouse.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -3 -c segment -g $VIDJIL_DIR/germline/mus-musculus.g $VIDJIL_DATA/example_mouse.fa
$ Segment sequence on IGK
1:segIGK.*IGKV.*IGKJ
......
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